Marianne Oelund posted a thread with links to her well executed NEF 12bit test comparing D2X, D300 and D3 at ISO100 and 200, taken both indoors and outdoors.
By popular request: D2X/D3/D300 low ISO comparison



I have converted the ISO100 NEF files in Nikon CaptureNX, where I removed sharpening in Base Adjustments and added an USM sharpening edit step 50,5,1.
Otherwise I didn't change anything in the conversion. Link to the threads I posted at dpreview:
Comparison ISO100 D2X D300 D3 (D3/D2/D1 forum)
Comparison ISO100 D2X D300 D3 (D300/D200/D100 forum)